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Sequencing of 50 Human Exomes Reveals Adaptation to High Altitude
Open accessAbstract
No Genetic Vertigo: Peoples living in high altitudes have adapted to their situation (see the Perspective by Storz ). To identify gene regions that might have contributed to high-altitude adaptation in Tibetans, Simonson et al. (p. 72 , published online 13 May) conducted a genome scan of nucleotide polymorphism comparing Tibetans, Han Chinese, and Japanese, while Yi et al. (p. 75 ) performed comparable analyses on the coding regions of all genes—their exomes. Both studies converged on a gene, endothelial Per-Arnt-Sim domain protein 1 (also known as hypoxia-inducible factor 2 α), which has been linked to the regulation of red blood cell production. Other genes identified that were potentially under selection included adult and fetal hemoglobin and two functional candidate loci that were correlated with low hemoglobin concentration in Tibetans. Future detailed functional studies will now be required to examine the mechanistic underpinnings of physiological adaptation to high altitudes.
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“For example, by studying genes that show population-specific allele-frequency differences between Tibetans and Han Chinese, a signal of positive natural selection was detected in EPAS1, a transcription factor involved in the response to hypoxia, which most probably helps the Tibetans to live at high altitudes [40].”
From Ancient DNA and the rewriting of human history: be sparing with Occam’s razor (2016) · cites this paper as [40]
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“Genome-wide searches for single-nucleotide polymorphisms (SNP), candidate gene approaches and exome sequencing have identified genetic variations in the HIF2A, PHD2 and PPARA genes that associate with lower hemoglobins in native Tibetans compared to Han Chinese and with high altitude adaptation in other populations.”
From Regulation of erythropoiesis by hypoxia-inducible factors (2013) · cites this paper as [173]
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Self-citationEvidence of widespread selection on standing variation in Europe at height-associated SNPs
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An oxygen-regulated switch in the protein synthesis machinery
Uniacke, J., Holterman, C. E., Lachance, G., Franovic, A., Jacob, M. D., Fabian, M. R., Payette, J., Holcik, M., Pause, A., & Lee, S. (2012) · Nature · doi:10.1038/nature11055 · Cited by 319
Climate and Urbanization Drive Mosquito Preference for Humans
Rose, N. H., Sylla, M., Badolo, A., Lutomiah, J., Ayala, D., Aribodor, O. B., Ibe, N., Akorli, J., Otoo, S., Mutebi, J.-P., et al. (2020) · Current Biology · doi:10.1016/j.cub.2020.06.092 · Cited by 319
West, J. B. (2012) · American Journal of Respiratory and Critical Care Medicine · doi:10.1164/rccm.201207-1323ci · Cited by 336
“Yi and colleagues (21) took another approach and limited their analysis to 50 exomes of Tibetans (i.”
BackgroundVarshney, R. K., Thudi, M., Roorkiwal, M., He, W., Upadhyaya, H. D., Yang, W. C., Bajaj, P., Cubry, P., Rathore, A., Jian, J., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0401-3 · Cited by 324
Self-citationRNA sequencing reveals the complex regulatory network in the maize kernel
Fu, J., Cheng, Y., Linghu, J., Yang, X., Kang, L., Zhang, Z., Zhang, J., He, C., Du, X., Peng, Z., et al. (2013) · Nature Communications · doi:10.1038/ncomms3832 · Cited by 299
Self-citationExome sequencing: the sweet spot before whole genomes
Teer, J. K., & Mullikin, J. C. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq333 · Cited by 303
“Researchers used whole exome capture to identify changes in allele frequency between high-altitude populations (Tibetans) and low altitude populations (Han Chinese and Danes) (38).”
MethodA Genome-Wide Search for Signals of High-Altitude Adaptation in Tibetans
Xu, S., Li, S., Yang, Y., Tan, J., Lou, H., Jin, W., Yang, L., Pan, X., Wang, J., Shen, Y., et al. (2011) · Molecular Biology and Evolution · doi:10.1093/molbev/msq277 · Cited by 331
“S.X. was supported by the National Science Foundation of China (30971577) and the Science and Technology Commission of Shanghai Municipality (09ZR1436400).”
BackgroundInfluentialSelf-citationAdmixture into and within sub-Saharan Africa
Busby, G., Band, G., Le, S. Q., Jallow, M., Bougama, E., Mangano, V. D., Amenga-Etego, L. N.-K., Enimil, A. K., Apinjoh, T. O., Ndila, C., et al. (2016) · eLife · doi:10.7554/elife.15266 · Cited by 293
“, 2013); EPAS1 and EGLN1 in Tibetans (Yi et al., 2010); and at a separate loci within EGLN1 in Andean groups (Bigham et al.”
BackgroundThe genetics of monarch butterfly migration and warning colouration
Zhan, S., Zhang, W., Niitepõld, K., Hsu, J. L., Haeger, J. F., Zalucki, M. P., Altizer, S., de Roode, J. C., Reppert, S. M., & Kronforst, M. R. (2014) · Nature · doi:10.1038/nature13812 · Cited by 295
Genome-culture coevolution promotes rapid divergence of killer whale ecotypes
Foote, A. D., Vijay, N., Ávila‐Arcos, M. C., Baird, R. W., Durban, J. W., Fumagalli, M., Gibbs, R. A., Hanson, M. B., Korneliussen, T. S., Martin, M. D., et al. (2016) · Nature Communications · doi:10.1038/ncomms11693 · Cited by 301
Self-citationHIF prolyl hydroxylase inhibitors for the treatment of renal anaemia and beyond
Maxwell, P. H., & Eckardt, K. (2015) · Nature Reviews Nephrology · doi:10.1038/nrneph.2015.193 · Cited by 288
PHENOTYPIC PLASTICITY AND EPIGENETIC MARKING: AN ASSESSMENT OF EVIDENCE FOR GENETIC ACCOMMODATION
Schlichting, C. D., & Wund, M. A. (2014) · Evolution · doi:10.1111/evo.12348 · Cited by 295
“Variants of EGLN1, which degrades HIF under normal conditions, are under positive selection in both Tibetan and Andean samples, whereas Tibetan EPAS1 is under very strong selection (Bigham et al. 2010; Yi et al. 2010; Xiang et al. 2013).”
BackgroundKorneliussen, T. S., Moltke, I., Albrechtsen, A., & Nielsen, R. (2013) · BMC Bioinformatics · doi:10.1186/1471-2105-14-289 · Cited by 269
“Pr(D | x = j) can be calculated fast using a dynamic programming algorithm described in detail in references [33,35], and we refer readers to these publications for details.”
MethodSelf-citationDraft genome sequence of the Tibetan antelope
Ge, R.-L., Cai, Q., Shen, Y., San, A., Ma, L., Zhang, Y., Yi, X., Chen, Y., Yang, L., Huang, Y., et al. (2013) · Nature Communications · doi:10.1038/ncomms2860 · Cited by 280
Self-citationAdaptive introgression enables evolutionary rescue from extreme environmental pollution
Oziolor, E. M., Reid, N. M., Yair, S., Lee, K. M., VerPloeg, S. L. G., Bruns, P. C., Shaw, J. R., Whitehead, A., & Matson, C. W. (2019) · Science · doi:10.1126/science.aav4155 · Cited by 286
Dispersals and genetic adaptation of Bantu-speaking populations in Africa and North America
Patin, É., Lopez, M., Grollemund, R., Verdu, P., Harmant, C., Quach, H., Laval, G., Perry, G. H., Barreiro, L. B., Froment, A., et al. (2017) · Science · doi:10.1126/science.aal1988 · Cited by 284
Ancestral Origins and Genetic History of Tibetan Highlanders
Lu, D., Lou, H., Yuan, K., Wang, X., Wang, Y., Zhang, C., Lü, Y., Yang, X. W., Deng, L., Zhou, Y., et al. (2016) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.07.002 · Cited by 276
“A recent genetic study utilizing exome sequencing data estimated a divergence time of 2,750 years between Tibetans and Han Chinese.(4) Existing archaeological and genetic data are not sufficient to address the discrepancy between times estimated by different studies.”
BackgroundMethodResultInfluentialSelf-citationChen, C.-H., Yang, J.-H., Chiang, C. W. K., Hsiung, C., Wu, P., Chang, L.-C., Chu, H., Chang, J., Song, I.-W., Yang, S.-L., et al. (2016) · Human Molecular Genetics · doi:10.1093/hmg/ddw346 · Cited by 274
“Although the effect is likely not nearly as strong, this is reminiscent of the high-altitude adaptation in Han and Tibetan Chinese (32).”
BackgroundSelf-citationDistance from sub-Saharan Africa predicts mutational load in diverse human genomes
Henn, B. M., Botigué, L. R., Peischl, S., Dupanloup, I., Lipatov, M., Maples, B. K., Martin, A. R., Musharoff, S. A., Cann, H. M., Snyder, M. P., et al. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1510805112 · Cited by 268
“Others have emphasized evidence for pervasive adaptive selection(53, 54) and a variety of studies have identified specific beneficial alleles locally adapted to high altitude, immune response and pigmentation(55-57).”
BackgroundRossier, B. C., Baker, M. E., & Studer, R. A. (2015) · Physiological Reviews · doi:10.1152/physrev.00011.2014 · Cited by 269
“Another case is that of a gene, EPAS1 or HIF2 (coding for a transcription factor involved in hemoglobin concentration), conferring resistance to hypoxia to populations living at high elevation (Tibetan, Andean) (22, 350).”
BackgroundBi, K., Vanderpool, D., Singhal, S., Linderoth, T. P., Moritz, C. C., & Good, J. M. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-403 · Cited by 267
“Since genotype calling is not a focus of the present paper, we did not perform quality score recalibration but related information can be found in [4] and [23].”
BackgroundGünther, T., Malmström, H., Svensson, E., Omrak, A., Sánchez‐Quinto, F., Kılınç, G. M., Krzewińska, M., Eriksson, G., Fraser, M., Edlund, H., et al. (2018) · PLoS Biology · doi:10.1371/journal.pbio.2003703 · Cited by 256
Hypoxia-induced signaling in the cardiovascular system: pathogenesis and therapeutic targets
Zhao, Y., Xiong, W., Li, C., Zhao, R., Lu, H., Song, S., Zhou, Y., Hu, Y., Shi, B., & Ge, J. (2023) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-023-01652-9 · Cited by 275
Qi, X., Cui, C., Peng, Y., Zhang, X., Yang, Z., Zhong, H., Zhang, H., Xiang, K., Cao, X., Wang, Y., et al. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst093 · Cited by 258
Self-citationHumans at high altitude: Hypoxia and fetal growth
Moore, L. G., Charles, S. M., & Julian, C. G. (2011) · Respiratory Physiology & Neurobiology · doi:10.1016/j.resp.2011.04.017 · Cited by 251
“…scan of Tibetans with lowland Han: EPAS1 Endothelial PAS domain protein 1; also called ECYT4, HIF2A, HLF, MOP2, PASD2, bHLHe73 2p21-p16 (Yi et al., 2010) Sequencing 50 exomes in Tibetans, encompassing 92% of coding genes: EPAS1 Endothelial PAS domain protein 1; also called ECYT4,…”
BackgroundGenetic signatures of high-altitude adaptation in Tibetans
Yang, J., Jin, Z., Chen, J., Huang, X., Li, X., Liang, Y., Mao, J.-Y., Chen, X., Zheng, Z., Bakshi, A., et al. (2017) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1617042114 · Cited by 258
“In our study, we found that the signal of selection at the PPARA was not genome-wide significant (PMLMA-LOCO = 9.1 × 10 −5 at the top SNP rs149670586) and did not find any evidence that rs149670586 is associated with HGB (PGWAS = 0.20).”
BackgroundMethodResultInfluentialSelf-citationBunn, H. F. (2013) · Cold Spring Harbor Perspectives in Medicine · doi:10.1101/cshperspect.a011619 · Cited by 234
“The lead compounds that are currently undergoing clinical trials appear to inhibit HIF-2a specifically.”
BackgroundInfluentialWIT, P. J. G. M. D., Pespeni, M. H., Ladner, J. T., Barshis, D. J., Seneca, F., Jaris, H., Therkildsen, N. O., Morikawa, M. K., & Palumbi, S. R. (2012) · Molecular Ecology Resources · doi:10.1111/1755-0998.12003 · Cited by 246
“…reasonable cost and are currently revolutionizing our view of many important biological concepts, such as natural selection (Pickrell et al. 2009; Yi et al. 2010; Pespeni et al. 2011), gene flow (Tishkoff et al. 2009; Neafsey et al. 2010) and gene expression patterns (Wolf et al. 2010; Renaut &…”
BackgroundLarge-Scale Whole-Genome Sequencing of Three Diverse Asian Populations in Singapore
Wu, D., Dou, J., Chai, X., Bellis, C., Wilm, A., Shih, C. C., Soon, W. W., Bertin, N., Lin, C. B., Khor, C. C., et al. (2019) · Cell · doi:10.1016/j.cell.2019.09.019 · Cited by 241
Self-citationInfant and child death in the human environment of evolutionary adaptation
Volk, A. A., & Atkinson, J. (2013) · Evolution and Human Behavior · doi:10.1016/j.evolhumbehav.2012.11.007 · Cited by 238
“However, it is important to note that recent theories suggest that the last 10,000 years have played a significant role as a source of evolutionary adaptations and are hence part of the human EEA (Cochran & Harpending, 2009; Hartl & Clark, 1997; Irons, 1998; Yi et al., 2010; Tishkoff et al., 2007).”
BackgroundZhang, J., Jima, D. D., Moffitt, A. B., Liu, Q., Czader, M., Hsi, E. D., Fedoriw, Y. D., Dunphy, C. H., Richards, K. L., Gill, J., et al. (2014) · Blood · doi:10.1182/blood-2013-07-517177 · Cited by 249
Admixture facilitates genetic adaptations to high altitude in Tibet
Jeong, C., Alkorta‐Aranburu, G., Basnyat, B., Neupane, M., Witonsky, D., Pritchard, J. K., Beall, C. M., & Rienzo, A. D. (2014) · Nature Communications · doi:10.1038/ncomms4281 · Cited by 247
Genetic Screen for Cell Fitness in High or Low Oxygen Highlights Mitochondrial and Lipid Metabolism
Jain, I. H., Calvo, S. E., Markhard, A. L., Skinner, O. S., To, T.-L., Ast, T., & Mootha, V. K. (2020) · Cell · doi:10.1016/j.cell.2020.03.029 · Cited by 224
“These studies have identified polymorphisms in the canonical vHL-PHD-HIF O2 sensing pathways (Beall et al., 2010; Peng et al., 2011; Simonson et al., 2010; Xu et al., 2011; Yang et al., 2017; Yi et al., 2010), representing the most rapid known example of recent natural selection.”
Ancient genomic changes associated with domestication of the horse
Librado, P., Gamba, C., Gaunitz, C., Sarkissian, C. S. I. D., Pruvost, M., Albrechtsen, A., Fages, A., Khan, N., Schubert, M., Jagannathan, V., et al. (2017) · Science · doi:10.1126/science.aam5298 · Cited by 231
Genetic Signatures Reveal High-Altitude Adaptation in a Set of Ethiopian Populations
Huerta‐Sánchez, E., DeGiorgio, M., Pagani, L., Tarekegn, A., Ekong, R., Antão, T., Cardona, A., Montgomery, H., Cavalleri, G. L., Robbins, P. A., et al. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst089 · Cited by 223
“…genes within the HIF hypoxia-sensing pathway exhibiting strong signatures of positive selection in response to high altitude have been identified (e.g., EPAS1 and EGLN1; Beall et al. 2010; Bigham et al. 2010; Simonson et al. 2010; Yi et al. 2010; Peng et al. 2011; Wang et al. 2011; Xu et al. 2011).”
BackgroundMethodInfluentialSelf-citationPopulation genomics based on low coverage sequencing: how low should we go?
Buerkle, C. A., & Gompert, Z. (2012) · Molecular Ecology · doi:10.1111/mec.12105 · Cited by 220
“…analyses utilize allele frequencies or other population parameters, including their comparison between samples from different natural populations, experimental treatments or phenotypic categories (e.g., Burke et al. 2010; Simonson et al. 2010; Turner et al. 2010; Yi et al. 2010; Jones et al. 2012).”
BackgroundGou, X., Wang, Z., Li, N., Qiu, F., Xu, Z., Yan, D., Yang, S., Jia, J., Kong, X., Wei, Z., et al. (2014) · Genome Research · doi:10.1101/gr.171876.113 · Cited by 216
“…have been performed for three typical highland populations including Tibetans (Beall et al. 2010; Bigham et al. 2010; Simonson et al. 2010; Yi et al. 2010; Peng et al. 2011; Xu et al. 2011), Andeans (Bigham et al. 2009, 2010), and Ethiopians (Alkorta-Aranburu et al. 2012; Scheinfeldt et…”
BackgroundInfluentialSelf-citationJeong, C., Ozga, A. T., Witonsky, D., Malmström, H., Edlund, H., Hofman, C. A., Hagan, R. W., Jakobsson, M., Lewis, C. M., Aldenderfer, M. S., et al. (2016) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1520844113 · Cited by 211
“Consequently, the subsequent selection of this haplotype in humans is difficult to model using genetic data from living populations, and dates ranging from 2,750 ya to 18,250 ya have been proposed (13, 17, 38).”
Method
Metadata
- Authors
- Yi, X., Liang, Y., Huerta-Sanchez, E., Jin, X., Cuo, Z. X. P., Pool, J. E., Xu, X., Jiang, H., Vinckenbosch, N., Korneliussen, T. S., Zheng, H., Liu, T., He, W., Li, K., Luo, R., Nie, X., Wu, H., Zhao, M., Cao, H., Zou, J., Shan, Y., Li, S., Yang, Q., Asan, Ni, P., Tian, G., Xu, J., Liu, X., Jiang, T., Wu, R., Zhou, G., Tang, M., Qin, J., Wang, T., Feng, S., Li, G., Huasang, Luosang, J., Wang, W., Chen, F., Wang, Y., Zheng, X., Li, Z., Bianba, Z., Yang, G., Wang, X., Tang, S., Gao, G., Chen, Y., Luo, Z., Gusang, L., Cao, Z., Zhang, Q., Ouyang, W., Ren, X., Liang, H., Zheng, H., Huang, Y., Li, J., Bolund, L., Kristiansen, K., Li, Y., Zhang, Y., Zhang, X., Li, R., Li, S., Yang, H., Nielsen, R., Wang, J., & Wang, J.
- Affiliations
- BGI Group (China) (CN)
- Department of Integrative Biology and Department of Statistics, University of California Berkeley, Berkeley, CA 94820, USA.
- Tibet Autonomous Region People's Hospital (CN)
- University of California, Davis (US)
- University of California, Berkeley (US)
- University of Copenhagen (DK)
- The Military General Hospital of Tibet, Lhasa, 850007, China.
- The hospital of XiShuangBanNa Dai Nationalities, Autonomous Jinghong 666100, Yunnan, China.
- Corresponding author
- Yi, Xin
- Liang, Yu
- Jin, Xin
- Cuo, Zha Xi Ping
- Pool, John E.
- ORCID
- Yi, Xin
- Liang, Yu
- Jin, Xin
- Pool, John E.
- Xu, Xun
- Jiang, Hui
- Korneliussen, Thorfinn Sand
- Zheng, Hancheng
- Liu, Tao
- He, Weiming
- Luo, Ruibang
- Wu, Honglong
- Cao, Hongzhi
- Zou, Jing
- Shan, Ying
- Yang, Qi
- Tian, Geng
- Xu, Junming
- Liu, Xiao
- Wu, Renhua
- Zhou, Guangyu
- Tang, Meifang
- Qin, Junjie
- Wang, Tong
- Wang, Wei
- Chen, Fang
- Li, Zhuo
- Yang, Ge
- Tang, Shuhui
- Gao, Guoyi
- Luo, Zhen
- Gusang, Lamu
- Zhang, Qinghui
- Liang, Huiqing
- Bolund, Lars
- Kristiansen, Karsten
- Li, Yingrui
- Zhang, Yong
- Zhang, Xiuqing
- Li, Ruiqiang
- Li, Songgang
- Yang, Huanming
- Nielsen, Rasmus
- Wang, Jun
- Wang, Jian
- Venue
- Science
- Published
- 2010-07-02
- Volume
- 329
- Issue
- 5987
- Pages
- 75-78
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC3711608
- OpenAlex
- W2147575903
- Cited by
- 1,611
- References
- 35
- Citations by year
- 2026: 92 · 2025: 95 · 2024: 90 · 2023: 123 · 2022: 113 · 2021: 123 · 2020: 101 · 2019: 106 · 2018: 84 · 2017: 88 · 2016: 105 · 2015: 111 · 2014: 95 · 2013: 97 · 2012: 90
- FWCI
- 50.78
- Type
- journal article
- Language
- en
- Open access
- green
- europepmc.org
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- The HKU Scholars Hub (University of Hong Kong) (submittedVersion)
- Research at the University of Copenhagen (University of Copenhagen) (submittedVersion)
- Funders
- Schweizerischer Nationalfonds zur Förderung der Wissenschaftlichen Forschung (124318)
- U.S. Public Health Service (R01-MHG084695)
- National Institute on Alcohol Abuse and Alcoholism (R21AA022707)
- National Institute of Mental Health (R01MH084695)
- National Human Genome Research Institute (R01HG003229)
- Topics
- Health Sciences › Medicine › Physiology (medical) › High Altitude and Hypoxia
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Forensic and Genetic Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Evolution and Genetic Dynamics
- Keywords
- high-altitude adaptation, Tibetan Plateau, EPAS1, natural selection, hypoxia response, allele frequency change, single nucleotide polymorphisms, Han Chinese, population genomics, exome sequencing
- MeSH terms
- Acclimatization, Endothelial PAS Domain-Containing Protein 1, Altitude, Bayes Theorem, China, Erythrocyte Count, Ethnicity, Exons, Female, Gene Frequency, Hemoglobins, Humans, Male, Oxygen, Selection, Genetic, Genome, Human, Sequence Analysis, DNA, Tibet, Polymorphism, Single Nucleotide, Asian People, Basic Helix-Loop-Helix Proteins, Basic Helix-Loop-Helix Transcription Factors, Genetic Association Studies
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